Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 118 of 279
Found at i:37513336 original size:23 final size:23
Alignment explanation
Indices: 37513310--37513354 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
37513300 TGGGTATGTG
*
37513310 ATGACGTTATCTT-ATAAATATGC
1 ATGAAGTTATCTTGA-AAATATGC
*
37513333 ATGAATTTATCTTGAAAATATG
1 ATGAAGTTATCTTGAAAATATG
37513355 TTGAATTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (23 bp):
ATGAAGTTATCTTGAAAATATGC
Found at i:37516858 original size:39 final size:39
Alignment explanation
Indices: 37516815--37516893 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
37516805 CCAGACATAT
*
37516815 TTCCAGCACGTAGCCTGCGGACCTTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
37516854 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
1 TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
37516893 T
1 T
37516894 CACTGAATGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (39 bp):
TTCCAGCACATAGCCTGCGGACCTTAAGTCCGGATATAA
Found at i:37525205 original size:11 final size:11
Alignment explanation
Indices: 37525186--37525227 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
37525176 TCAAAATAGG
37525186 AAAAA-AAAAT
1 AAAAATAAAAT
*
37525196 AAACATAAAAT
1 AAAAATAAAAT
37525207 AAAAATAAACAT
1 AAAAATAAA-AT
*
37525219 AAAGATAAA
1 AAAAATAAA
37525228 TGGACTCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 4 0.15
11 13 0.48
12 10 0.37
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:37525212 original size:17 final size:17
Alignment explanation
Indices: 37525186--37525227 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
37525176 TCAAAATAGG
37525186 AAAA-AAAAATAAACAT
1 AAAATAAAAATAAACAT
37525202 AAAATAAAAATAAACAT
1 AAAATAAAAATAAACAT
37525219 AAAGATAAA
1 AAA-ATAAA
37525228 TGGACTCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 4 0.17
17 15 0.62
18 5 0.21
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (17 bp):
AAAATAAAAATAAACAT
Found at i:37525226 original size:23 final size:21
Alignment explanation
Indices: 37525186--37525227 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
37525176 TCAAAATAGG
37525186 AAAAAAAAATAAACATAAAAT
1 AAAAAAAAATAAACATAAAAT
*
37525207 AAAAATAAACATAAAGATAAA
1 AAAAA-AAA-ATAAACATAAA
37525228 TGGACTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (21 bp):
AAAAAAAAATAAACATAAAAT
Found at i:37526289 original size:101 final size:101
Alignment explanation
Indices: 37526113--37526314 Score: 377
Period size: 101 Copynumber: 2.0 Consensus size: 101
37526103 GGGAAGCTAA
*
37526113 ATTAAGAGTGGTTGCGAAGCTGGCTTTAAATAGAGGGAACCATGAGGAGAGTAAAGGTACCTTTT
1 ATTAAGAGTGGTTGCGAAGCTGGCTTTAAATAGAGGGAACCATGAGGAGAGTAAAGGGACCTTTT
37526178 CATGGATGATCCCTTTCGCTGTATGGCGTGCTCGTT
66 CATGGATGATCCCTTTCGCTGTATGGCGTGCTCGTT
37526214 ATTAAGAGTGGTTGCGAAGCTGGCTTTAAATAGAGGGAACCATGAGGAGAGTAAAGGGACCTTTT
1 ATTAAGAGTGGTTGCGAAGCTGGCTTTAAATAGAGGGAACCATGAGGAGAGTAAAGGGACCTTTT
* *
37526279 CTTGGCTGATCCCTTTCGCTGTATGGCGTGCTCGTT
66 CATGGATGATCCCTTTCGCTGTATGGCGTGCTCGTT
37526315 TGGGTTGGGC
Statistics
Matches: 98, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 98 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (101 bp):
ATTAAGAGTGGTTGCGAAGCTGGCTTTAAATAGAGGGAACCATGAGGAGAGTAAAGGGACCTTTT
CATGGATGATCCCTTTCGCTGTATGGCGTGCTCGTT
Found at i:37526683 original size:27 final size:27
Alignment explanation
Indices: 37526653--37526715 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
37526643 TATTGAAATG
* *
37526653 CCCTCGATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTACCATTTCA
*
37526680 CCCTCGATTTATAGAATTACCGTTTCA
1 CCCTCGATTTATAGAATTACCATTTCA
37526707 CCCTCGATT
1 CCCTCGATT
37526716 ATGTTTAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.24, C:0.27, G:0.11, T:0.38
Consensus pattern (27 bp):
CCCTCGATTTATAGAATTACCATTTCA
Found at i:37526737 original size:101 final size:100
Alignment explanation
Indices: 37526616--37526815 Score: 346
Period size: 101 Copynumber: 2.0 Consensus size: 100
37526606 TTGTTATCCC
* *
37526616 TGTTTAGAATACTTTAGTTTACCAAATTATTGAAATGCCCTCGATTTGTAGAATTACCATTTTAC
1 TGTTTAGAATACTTTAGTTTACCAAATTACTGAAATGCCCTCAATTTGTAGAATTACCATTTTA-
37526681 CCTCGATTTATAGAATTACCGTTTCACCCTCGATTA
65 CCTCGATTTATAGAATTACCGTTTCACCCTCGATTA
*
37526717 TGTTTAGAATACTTTAGTTTACCAATTTACTGAAATGCCCTCAATTTGTAGAATTACCATTTTAC
1 TGTTTAGAATACTTTAGTTTACCAAATTACTGAAATGCCCTCAATTTGTAGAATTACCATTTTAC
* *
37526782 CTTGATTTATAGAATTATCGTTTCACCCTCGATT
66 CTCGATTTATAGAATTACCGTTTCACCCTCGATT
37526816 TACAAAATTA
Statistics
Matches: 94, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 33 0.35
101 61 0.65
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (100 bp):
TGTTTAGAATACTTTAGTTTACCAAATTACTGAAATGCCCTCAATTTGTAGAATTACCATTTTAC
CTCGATTTATAGAATTACCGTTTCACCCTCGATTA
Found at i:37526824 original size:27 final size:26
Alignment explanation
Indices: 37526754--37526869 Score: 117
Period size: 27 Copynumber: 4.3 Consensus size: 26
37526744 TACTGAAATG
* *
37526754 CCCTCAATTTGTAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTA-CATTTTA
* * *
37526781 -CCTTGATTTATAGAATTATCGTTTCA
1 CCCTCGATTTATAGAATTA-CATTTTA
* *
37526807 CCCTCGATTTACAAAATTACAATTTTA
1 CCCTCGATTTATAGAATTAC-ATTTTA
*
37526834 CCCTCAATTTATAGAATTACCATTTTA
1 CCCTCGATTTATAGAATTA-CATTTTA
37526861 CCCTCGATT
1 CCCTCGATT
37526870 GTGAAATTAC
Statistics
Matches: 71, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
26 21 0.30
27 49 0.69
28 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (26 bp):
CCCTCGATTTATAGAATTACATTTTA
Found at i:37526864 original size:54 final size:53
Alignment explanation
Indices: 37526768--37526869 Score: 141
Period size: 54 Copynumber: 1.9 Consensus size: 53
37526758 CAATTTGTAG
* ** * *
37526768 AATTACCATTTTACCTTGATTTATAGAATTATCGTTTCACCCTCGATTTACAA
1 AATTACAATTTTACCTCAATTTATAGAATTACCATTTCACCCTCGATTTACAA
*
37526821 AATTACAATTTTACCCTCAATTTATAGAATTACCATTTTACCCTCGATT
1 AATTACAATTTTA-CCTCAATTTATAGAATTACCATTTCACCCTCGATT
37526870 GTGAAATTAC
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
53 12 0.29
54 30 0.71
ACGTcount: A:0.31, C:0.22, G:0.06, T:0.41
Consensus pattern (53 bp):
AATTACAATTTTACCTCAATTTATAGAATTACCATTTCACCCTCGATTTACAA
Found at i:37526891 original size:27 final size:26
Alignment explanation
Indices: 37526861--37527024 Score: 93
Period size: 27 Copynumber: 6.1 Consensus size: 26
37526851 TACCATTTTA
* **
37526861 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
* *
37526888 CCCTG-TAGGATAAAATTATCAAAATAC
1 CCCTGAT-TG-TAAAATTACCAAAATAC
*
37526915 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTAAAATTACCAAAATAC
** * * *
37526942 CAATGGTTTGTGAAATTACCGAAATA-
1 CCCT-GATTGTAAAATTACCAAAATAC
* *
37526968 CCCTCAATTTGTAAAATTACAAAAATAC
1 CCCT-GA-TTGTAAAATTACCAAAATAC
37526996 CCCTGATT-TACAAAATTA-CAGAAATAC
1 CCCTGATTGT--AAAATTACCA-AAATAC
37527023 CC
1 CC
37527025 TTGACTTTTT
Statistics
Matches: 106, Mismatches: 22, Indels: 18
0.73 0.15 0.12
Matches are distributed among these distances:
25 2 0.02
26 7 0.07
27 90 0.85
28 6 0.06
29 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (26 bp):
CCCTGATTGTAAAATTACCAAAATAC
Found at i:37526942 original size:54 final size:53
Alignment explanation
Indices: 37526859--37527000 Score: 126
Period size: 54 Copynumber: 2.7 Consensus size: 53
37526849 ATTACCATTT
* * ** *
37526859 TACCCTCGA-TTGTGAAATTACTGAAATACCCCTGTAGGATAAAATTATCAAAA
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTGTAGG-TAAAATTACCAAAA
* * ** ** * *
37526912 TACCC-CTAGTTTGTAAAATTACCAAAATACCAATGGTTTGTGAAATTACCGAAA
1 TACCCTC-AATTTGTAAAATTACAAAAATACCCCT-GTAGGTAAAATTACCAAAA
37526966 TACCCTCAATTTGTAAAATTACAAAAATACCCCTG
1 TACCCTCAATTTGTAAAATTACAAAAATACCCCTG
37527001 ATTTACAAAA
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
52 1 0.01
53 6 0.09
54 58 0.84
55 4 0.06
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.29
Consensus pattern (53 bp):
TACCCTCAATTTGTAAAATTACAAAAATACCCCTGTAGGTAAAATTACCAAAA
Found at i:37527232 original size:27 final size:28
Alignment explanation
Indices: 37526898--37527304 Score: 180
Period size: 27 Copynumber: 14.8 Consensus size: 28
37526888 CCCTGTAGGA
* *
37526898 TAAAATTATCAAAATACCCCT-AGTTTG
1 TAAAATTACCAAAATACCCTTGAGTTTG
**
37526925 TAAAATTACCAAAATACCAATG-GTTTG
1 TAAAATTACCAAAATACCCTTGAGTTTG
* * * *
37526952 TGAAATTACCGAAATACCC-TCAATTTG
1 TAAAATTACCAAAATACCCTTGAGTTTG
* * *
37526979 TAAAATTACAAAAATACCCCTGA-TTTA
1 TAAAATTACCAAAATACCCTTGAGTTTG
* * *
37527006 CAAAATTA-CAGAAATACCCTTGACTTTT
1 TAAAATTACCA-AAATACCCTTGAGTTTG
* * * *
37527034 TGAAAATTA-TAGAAATGCCATT-AGTTTA
1 T-AAAATTACCA-AAATACCCTTGAGTTTG
* ***
37527062 CAAAATTATTGAAATACCCTTG-GTTTG
1 TAAAATTACCAAAATACCCTTGAGTTTG
* * *
37527089 TAGATTTACCAAAACACCCTTGTTTAGTTTG
1 TAAAATTACCAAAATACCCTTG---AGTTTG
*
37527120 TAAAATTACCAAAATACCAC-TG-GTTTA
1 TAAAATTACCAAAATACC-CTTGAGTTTG
* * ** *
37527147 TGAAATTACCGAAATACCC-CCAATTTG
1 TAAAATTACCAAAATACCCTTGAGTTTG
** * *
37527174 TAAAATTATAAAAATACCCCTGA-TTTA
1 TAAAATTACCAAAATACCCTTGAGTTTG
* * *
37527201 CAAAATTA-CAAAATACCCTTGACTTTT
1 TAAAATTACCAAAATACCCTTGAGTTTG
* * * *
37527228 TAAAAATTA-TAGAAATACCATT-AGATTA
1 T-AAAATTACCA-AAATACCCTTGAGTTTG
* ** *
37527256 CAAAATTACTGAAATACCCCTG-GTTTG
1 TAAAATTACCAAAATACCCTTGAGTTTG
* * *
37527283 TAGATTTACCAAAACACCCTTG
1 TAAAATTACCAAAATACCCTTG
37527305 TAGGATGAAA
Statistics
Matches: 285, Mismatches: 75, Indels: 40
0.71 0.19 0.10
Matches are distributed among these distances:
26 15 0.05
27 198 0.69
28 23 0.08
29 26 0.09
31 22 0.08
32 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (28 bp):
TAAAATTACCAAAATACCCTTGAGTTTG
Found at i:37527303 original size:194 final size:195
Alignment explanation
Indices: 37526918--37527305 Score: 688
Period size: 195 Copynumber: 2.0 Consensus size: 195
37526908 AAAATACCCC
* *
37526918 TAGTTTGTAAAATTACCAAAATACCAATGGTTTGTGAAATTACCGAAATACCCTCAATTTGTAAA
1 TAGTTTGTAAAATTACCAAAATACCAATGGTTTATGAAATTACCGAAATACCCCCAATTTGTAAA
*
37526983 ATTACAAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGACTTTTTGAAAATTATAGAA
66 ATTACAAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGACTTTTTAAAAATTATAGAA
* * * *
37527048 ATGCCATTAGTTTACAAAATTATTGAAATACCCTTGGTTTGTAGATTTACCAAAACACCCTTGTT
131 ATACCATTAGATTACAAAATTACTGAAATACCCCTGGTTTGTAGATTTACCAAAACACCCTTGTT
*
37527113 TAGTTTGTAAAATTACCAAAATACCACTGGTTTATGAAATTACCGAAATACCCCCAATTTGTAAA
1 TAGTTTGTAAAATTACCAAAATACCAATGGTTTATGAAATTACCGAAATACCCCCAATTTGTAAA
*
37527178 ATTATAAAAATACCCCTGATTTACAAAATTACA-AAATACCCTTGACTTTTTAAAAATTATAGAA
66 ATTACAAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGACTTTTTAAAAATTATAGAA
37527242 ATACCATTAGATTACAAAATTACTGAAATACCCCTGGTTTGTAGATTTACCAAAACACCCTTGT
131 ATACCATTAGATTACAAAATTACTGAAATACCCCTGGTTTGTAGATTTACCAAAACACCCTTGT
37527306 AGGATGAAAT
Statistics
Matches: 184, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
194 90 0.49
195 94 0.51
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (195 bp):
TAGTTTGTAAAATTACCAAAATACCAATGGTTTATGAAATTACCGAAATACCCCCAATTTGTAAA
ATTACAAAAATACCCCTGATTTACAAAATTACAGAAATACCCTTGACTTTTTAAAAATTATAGAA
ATACCATTAGATTACAAAATTACTGAAATACCCCTGGTTTGTAGATTTACCAAAACACCCTTGTT
Found at i:37527365 original size:27 final size:27
Alignment explanation
Indices: 37527322--37527395 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
37527312 AAATGACTAA
*
37527322 AATACCCCTAATA-GGTAAAAAGACCGT
1 AATACCCCT-GTAGGGTAAAAAGACCGT
*
37527349 AA-AGCCCCTGTAGGGTAAAATGACCGT
1 AATA-CCCCTGTAGGGTAAAAAGACCGT
* *
37527376 AATACCCTTGTATGGTAAAA
1 AATACCCCTGTAGGGTAAAA
37527396 TGACGAATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 3 0.08
27 36 0.90
28 1 0.03
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAAAGACCGT
Found at i:37527410 original size:27 final size:28
Alignment explanation
Indices: 37527335--37527399 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 28
37527325 ACCCCTAATA
* *
37527335 GGTAAAAAGACCGTAA-AGCCCCTGTAG
1 GGTAAAATGACCGTAATAGCCCTTGTAG
*
37527362 GGTAAAATGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAATAGCCCTTGTAG
37527389 GGTAAAATGAC
1 GGTAAAATGAC
37527400 GAATATGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 33 0.97
28 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (28 bp):
GGTAAAATGACCGTAATAGCCCTTGTAG
Found at i:37527907 original size:168 final size:169
Alignment explanation
Indices: 37527586--37527921 Score: 568
Period size: 168 Copynumber: 2.0 Consensus size: 169
37527576 TGCTGAGAAG
37527586 CCGAAATGCTAAAATACCGGTATTTCAGGAACTTGTAATGTTGCGTATGGGTATAGATGCAATAA
1 CCGAAATGCTAAAATACCGGTATTTCAGGAACTTGTAATGTTGCGTATGGGTATAGATGCAATAA
* *
37527651 ATAAGATAAGATCGGTGTTTGGATCGATGGAACAGGTAAGAACTCAATTTTGTGCACGATGGTAA
66 ATAAGATAAGATCGGTGTTTGGATCGATGGAACAGGTAAAAACTCAATTTTGTGCACGATAGTAA
37527716 GTTGGGCCTCAATGGGCAGGAATTGGGCCAAATGGGCTA
131 GTTGGGCCTCAATGGGCAGGAATTGGGCCAAATGGGCTA
* * * *
37527755 CCGAAATGCTAAAATA-CTGTCATTTCGGGAACTTGTAATGTTGCGTGTGGGTATAGATGCGATA
1 CCGAAATGCTAAAATACCGGT-ATTTCAGGAACTTGTAATGTTGCGTATGGGTATAGATGCAATA
* * *
37527819 AATACGATAAGATC-GTGTTTGGATTGATGGAACGGGTAAAAACTCAATTTTGTGCACGATAGTA
65 AATAAGATAAGATCGGTGTTTGGATCGATGGAACAGGTAAAAACTCAATTTTGTGCACGATAGTA
37527883 AGTTGGGCCTCAATGGGCAGGAATTGGGCCAAATGGGCT
130 AGTTGGGCCTCAATGGGCAGGAATTGGGCCAAATGGGCT
37527922 TTTGGGCCCA
Statistics
Matches: 157, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
168 88 0.56
169 69 0.44
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.27
Consensus pattern (169 bp):
CCGAAATGCTAAAATACCGGTATTTCAGGAACTTGTAATGTTGCGTATGGGTATAGATGCAATAA
ATAAGATAAGATCGGTGTTTGGATCGATGGAACAGGTAAAAACTCAATTTTGTGCACGATAGTAA
GTTGGGCCTCAATGGGCAGGAATTGGGCCAAATGGGCTA
Found at i:37528409 original size:25 final size:26
Alignment explanation
Indices: 37528376--37528501 Score: 132
Period size: 25 Copynumber: 4.8 Consensus size: 26
37528366 AGGAAGTGCT
*
37528376 GAAAGGGCTCTGCCCCAGTTTACCGA
1 GAAAGGGCTTTGCCCCAGTTTACCGA
* *
37528402 -AAAGGGCTTTGCCTCAGTTTATCAGAAA
1 GAAAGGGCTTTGCCCCAGTTTA-CCG--A
*
37528430 GGGAAAGGGCTCTGCCCCAGTTTACCGA
1 --GAAAGGGCTTTGCCCCAGTTTACCGA
* *
37528458 -AAAGGGCTTTGCCTCAGTTTATC-A
1 GAAAGGGCTTTGCCCCAGTTTACCGA
37528482 GAAAGGGCTTTGCCCCAGTT
1 GAAAGGGCTTTGCCCCAGTT
37528502 ATTAAAAGAG
Statistics
Matches: 83, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.01
25 57 0.69
26 2 0.02
28 2 0.02
30 2 0.02
31 19 0.23
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (26 bp):
GAAAGGGCTTTGCCCCAGTTTACCGA
Found at i:37528462 original size:56 final size:56
Alignment explanation
Indices: 37528376--37528488 Score: 226
Period size: 56 Copynumber: 2.0 Consensus size: 56
37528366 AGGAAGTGCT
37528376 GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTTTGCCTCAGTTTATCAGAAAGG
1 GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTTTGCCTCAGTTTATCAGAAAGG
37528432 GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTTTGCCTCAGTTTATCAGAAAGG
1 GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTTTGCCTCAGTTTATCAGAAAGG
37528488 G
1 G
37528489 CTTTGCCCCA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 57 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (56 bp):
GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTTTGCCTCAGTTTATCAGAAAGG
Found at i:37528514 original size:24 final size:23
Alignment explanation
Indices: 37528433--37528528 Score: 84
Period size: 25 Copynumber: 3.9 Consensus size: 23
37528423 TCAGAAAGGG
* *
37528433 AAAGGGCTCTGCCCCAGTTTACCGA
1 AAAGGGCTTTGCCCCAG-TTATC-A
*
37528458 AAAGGGCTTTGCCTCAGTTTATCA
1 AAAGGGCTTTGCCCCAG-TTATCA
*
37528482 GAAAGGGCTTTGCCCCAGTTATTA
1 -AAAGGGCTTTGCCCCAGTTATCA
**
37528506 AAAGAGGCTAGGCCTCCAGTTAT
1 AAAG-GGCTTTGCC-CCAGTTAT
37528529 ATAATAAAGC
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
23 4 0.07
24 13 0.21
25 44 0.72
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (23 bp):
AAAGGGCTTTGCCCCAGTTATCA
Found at i:37528526 original size:50 final size:50
Alignment explanation
Indices: 37528376--37528526 Score: 153
Period size: 56 Copynumber: 2.9 Consensus size: 50
37528366 AGGAAGTGCT
**
37528376 GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTTTGCCTCAGTTTATCAGAAA
1 GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTAGGCCTCAGTTTATC----A
**
37528430 GGGAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTTTGCCTCAGTTTATCA
1 --GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTAGGCCTCAGTTTATCA
* **
37528482 GAAAGGGCTTTGCCCCAG-TTA-TTAAAAGAGGCTAGGCCTCCAGTT
1 GAAAGGGCTCTGCCCCAGTTTACCGAAAAG-GGCTAGGCCT-CAGTT
37528527 ATATAATAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 10
0.85 0.05 0.10
Matches are distributed among these distances:
48 5 0.06
49 11 0.12
50 22 0.25
52 1 0.01
56 49 0.56
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.25
Consensus pattern (50 bp):
GAAAGGGCTCTGCCCCAGTTTACCGAAAAGGGCTAGGCCTCAGTTTATCA
Found at i:37528861 original size:31 final size:31
Alignment explanation
Indices: 37528722--37528860 Score: 206
Period size: 31 Copynumber: 4.5 Consensus size: 31
37528712 TGTTTACAGT
37528722 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
37528753 AAAGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
37528784 AAAAGCTTCGGCCCAGTGAGATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* * * *
37528815 AAATGCTTCGGCCCAATGATATGGTTTATGG
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
* *
37528846 AAGGGCTTTGGCCCA
1 AAAGGCTTCGGCCCA
37528861 AATTGTACTG
Statistics
Matches: 98, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 98 1.00
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:37529119 original size:35 final size:35
Alignment explanation
Indices: 37529080--37529189 Score: 84
Period size: 35 Copynumber: 3.2 Consensus size: 35
37529070 ATTAATATTT
37529080 TTATTTGGTTTTGGGTTGTAATAAGGCCATTTTAA
1 TTATTTGGTTTTGGGTTGTAATAAGGCCATTTTAA
* * * * *** *
37529115 TTATTT--TTCTGGGAGTTTTATCTTA-TTAATATT-A
1 TTATTTGGTT-TTGG-GTTGTA-ATAAGGCCATTTTAA
*
37529149 TTACTTGGTTTTGGGTTGTAATAAGGCCATTTTAA
1 TTATTTGGTTTTGGGTTGTAATAAGGCCATTTTAA
37529184 TTATTT
1 TTATTT
37529190 TTCTGGGATT
Statistics
Matches: 50, Mismatches: 18, Indels: 14
0.61 0.22 0.17
Matches are distributed among these distances:
33 4 0.08
34 18 0.36
35 24 0.48
36 4 0.08
ACGTcount: A:0.23, C:0.06, G:0.18, T:0.53
Consensus pattern (35 bp):
TTATTTGGTTTTGGGTTGTAATAAGGCCATTTTAA
Found at i:37529132 original size:69 final size:69
Alignment explanation
Indices: 37529059--37529211 Score: 261
Period size: 69 Copynumber: 2.2 Consensus size: 69
37529049 TTTCTTTATA
* *
37529059 AGTTTTATCTTATTAATATTTTTATTTGGTTTTGGGTTGTAATAAGGCCATTTTAATTATTTTTC
1 AGTTTTATCTTATTAATATTATTACTTGGTTTTGGGTTGTAATAAGGCCATTTTAATTATTTTTC
37529124 TGGG
66 TGGG
37529128 AGTTTTATCTTATTAATATTATTACTTGGTTTTGGGTTGTAATAAGGCCATTTTAATTATTTTTC
1 AGTTTTATCTTATTAATATTATTACTTGGTTTTGGGTTGTAATAAGGCCATTTTAATTATTTTTC
37529193 TGGG
66 TGGG
*
37529197 ATTATTTTATCTTAT
1 A--GTTTTATCTTAT
37529212 ACCCTATATT
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
69 68 0.86
71 11 0.14
ACGTcount: A:0.23, C:0.07, G:0.16, T:0.55
Consensus pattern (69 bp):
AGTTTTATCTTATTAATATTATTACTTGGTTTTGGGTTGTAATAAGGCCATTTTAATTATTTTTC
TGGG
Found at i:37530004 original size:18 final size:20
Alignment explanation
Indices: 37529964--37530015 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
37529954 GGGTATAACT
*
37529964 CACGCCCGTGTGTCCGAACA
1 CACGGCCGTGTGTCCGAACA
37529984 CACGGCCGTGTGTCCGAACA
1 CACGGCCGTGTGTCCGAACA
37530004 CACGGCCGTGTG
1 CACGGCCGTGTG
37530016 CCTCGCCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.17, C:0.37, G:0.31, T:0.15
Consensus pattern (20 bp):
CACGGCCGTGTGTCCGAACA
Found at i:37532729 original size:17 final size:18
Alignment explanation
Indices: 37532709--37532743 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
37532699 AATAAATAAA
*
37532709 AATAAAAA-ATAAATTGC
1 AATAAAAATAAAAATTGC
37532726 AATAAAAATAAAAATTGC
1 AATAAAAATAAAAATTGC
37532744 TAAAGTAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (18 bp):
AATAAAAATAAAAATTGC
Found at i:37543813 original size:19 final size:19
Alignment explanation
Indices: 37543781--37543821 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
37543771 TACATATTAT
37543781 AAATATACAAATATATAAC
1 AAATATACAAATATATAAC
* *
37543800 AAATATATAGATATATAAC
1 AAATATACAAATATATAAC
37543819 AAA
1 AAA
37543822 GCATAAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.27
Consensus pattern (19 bp):
AAATATACAAATATATAAC
Found at i:37543838 original size:3 final size:3
Alignment explanation
Indices: 37543830--37543862 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
37543820 AAGCATAAAC
37543830 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
37543863 CATTGGAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:37545438 original size:43 final size:42
Alignment explanation
Indices: 37545391--37545515 Score: 135
Period size: 42 Copynumber: 2.9 Consensus size: 42
37545381 CCCAGACGTA
*
37545391 GTCTTACATGTAATCAAATATCGATGCCAATGTCCCAGACAGG
1 GTCTTACACGTAATCAAA-ATCGATGCCAATGTCCCAGACAGG
* * * *
37545434 GTCTTACACGAAATCAAACA-CGATGCCGATGACCCAGACATG
1 GTCTTACACGTAATCAAA-ATCGATGCCAATGTCCCAGACAGG
* * *
37545476 GTCTTACACCTAAATCATAAGTCGATGCCAACGTCCCAGA
1 GTCTTACACGT-AATCA-AAATCGATGCCAATGTCCCAGA
37545516 TGTGGTCTTA
Statistics
Matches: 67, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
42 28 0.42
43 22 0.33
44 17 0.25
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.22
Consensus pattern (42 bp):
GTCTTACACGTAATCAAAATCGATGCCAATGTCCCAGACAGG
Found at i:37545915 original size:8 final size:8
Alignment explanation
Indices: 37545902--37545926 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
37545892 AAATTACCCC
37545902 TCACATTT
1 TCACATTT
37545910 TCACATTT
1 TCACATTT
37545918 TCACATTT
1 TCACATTT
37545926 T
1 T
37545927 AGTCCCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.52
Consensus pattern (8 bp):
TCACATTT
Found at i:37551599 original size:25 final size:25
Alignment explanation
Indices: 37551565--37551614 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
37551555 TAAAGCTTAG
37551565 TAAGTTCGTATAACATTGAATTTAA
1 TAAGTTCGTATAACATTGAATTTAA
37551590 TAAGTTCGTATAACATTGAATTTAA
1 TAAGTTCGTATAACATTGAATTTAA
37551615 CTTACCAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (25 bp):
TAAGTTCGTATAACATTGAATTTAA
Found at i:37552084 original size:25 final size:25
Alignment explanation
Indices: 37552042--37552111 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
37552032 AGCTTTGGAG
* *
37552042 AGCCAA-TATCGGAAAGCTCCGGAA
1 AGCCAATTATCGGGAAGCTCCGAAA
* **
37552066 AGCC-ATTAATCTGGAAGCTCATAAA
1 AGCCAATT-ATCGGGAAGCTCCGAAA
37552091 AGCCAATTATCGGGAAGCTCC
1 AGCCAATTATCGGGAAGCTCC
37552112 AGAGAGCGAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
23 1 0.03
24 5 0.14
25 27 0.75
26 3 0.08
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (25 bp):
AGCCAATTATCGGGAAGCTCCGAAA
Found at i:37552142 original size:25 final size:25
Alignment explanation
Indices: 37552072--37552167 Score: 70
Period size: 25 Copynumber: 3.8 Consensus size: 25
37552062 GGAAAGCCAT
* * *
37552072 TAATCTGGAAGCTCATAAAAGCCAA
1 TAATCGGGAAGCTCATAAGAGCAAA
* *
37552097 TTATCGGGAAGCTCCA-GAGAGCGAAA
1 TAATCGGGAAGCT-CATAAGAGC-AAA
**
37552123 TAAT-GGGAAGCTCATAAGAGCCTA
1 TAATCGGGAAGCTCATAAGAGCAAA
* * *
37552147 TTATCGAGACGCTCATAAGAG
1 TAATCGGGAAGCTCATAAGAG
37552168 TTGTGGTGTG
Statistics
Matches: 55, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
24 6 0.11
25 42 0.76
26 7 0.13
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.20
Consensus pattern (25 bp):
TAATCGGGAAGCTCATAAGAGCAAA
Found at i:37554413 original size:40 final size:40
Alignment explanation
Indices: 37554354--37554565 Score: 259
Period size: 40 Copynumber: 5.3 Consensus size: 40
37554344 CATTTGAATG
*
37554354 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
37554394 TTATCCGGGTTAAGACCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
37554434 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
37554474 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * * * *
37554514 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
37554554 ATATCC-GGCTAA
1 ATATCCGGGCTAA
37554566 ATTCCGAAGA
Statistics
Matches: 151, Mismatches: 18, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
39 7 0.05
40 141 0.93
41 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:37556424 original size:19 final size:19
Alignment explanation
Indices: 37556400--37556438 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
37556390 ATTTTCTTCC
37556400 ATAAAACTTCATAATTCAT
1 ATAAAACTTCATAATTCAT
37556419 ATAAAACTTCATAATTCAT
1 ATAAAACTTCATAATTCAT
37556438 A
1 A
37556439 CATACTCATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAACTTCATAATTCAT
Found at i:37558258 original size:9 final size:9
Alignment explanation
Indices: 37558244--37558277 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
37558234 CAAAAAGTTT
37558244 ATTTTTACC
1 ATTTTTACC
* *
37558253 ATTTTTTCT
1 ATTTTTACC
37558262 ATTTTTACC
1 ATTTTTACC
37558271 ATTTTTA
1 ATTTTTA
37558278 AAATTTTGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTTTACC
Found at i:37558283 original size:18 final size:18
Alignment explanation
Indices: 37558244--37558284 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
37558234 CAAAAAGTTT
***
37558244 ATTTTTACCATTTTTTCT
1 ATTTTTACCATTTTTAAA
37558262 ATTTTTACCATTTTTAAA
1 ATTTTTACCATTTTTAAA
37558280 ATTTT
1 ATTTT
37558285 GTTGCCCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.63
Consensus pattern (18 bp):
ATTTTTACCATTTTTAAA
Found at i:37560110 original size:21 final size:21
Alignment explanation
Indices: 37560086--37560128 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
37560076 AATTCTTCTG
** *
37560086 AAGGTTAATGTTCCCCTTCCA
1 AAGGTTAAAATTCCACTTCCA
37560107 AAGGTTAAAATTCCACTTCCA
1 AAGGTTAAAATTCCACTTCCA
37560128 A
1 A
37560129 TAATTTTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.30
Consensus pattern (21 bp):
AAGGTTAAAATTCCACTTCCA
Found at i:37562831 original size:4 final size:4
Alignment explanation
Indices: 37562822--37562853 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
37562812 TTATGCATGG
37562822 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT
37562854 TGTTGCTTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:37567154 original size:31 final size:31
Alignment explanation
Indices: 37567119--37567179 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
37567109 AAGAATCTAA
* * *
37567119 TGACTTAAATAAAAAATTTTGAATAATTTAT
1 TGACTTAAACAAAAAAATTTAAATAATTTAT
37567150 TGACTTAAACAAAAAAATTTAAATAATTTA
1 TGACTTAAACAAAAAAATTTAAATAATTTA
37567180 ATACTTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (31 bp):
TGACTTAAACAAAAAAATTTAAATAATTTAT
Found at i:37568173 original size:18 final size:19
Alignment explanation
Indices: 37568132--37568167 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
37568122 AAAATTCATG
*
37568132 TATAATTTTAATATTTATC
1 TATATTTTTAATATTTATC
37568151 TATATTTTTAA-ATTTAT
1 TATATTTTTAATATTTAT
37568168 ACATATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTTTTAATATTTATC
Found at i:37575735 original size:19 final size:19
Alignment explanation
Indices: 37575711--37575749 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
37575701 GCTCGATTAT
*
37575711 TACTCTTTCCTCAGCACTC
1 TACTCTTTCCCCAGCACTC
37575730 TACTCTTTCCCCAGCACTC
1 TACTCTTTCCCCAGCACTC
37575749 T
1 T
37575750 CTAAAATGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.44, G:0.05, T:0.36
Consensus pattern (19 bp):
TACTCTTTCCCCAGCACTC
Found at i:37585330 original size:7 final size:7
Alignment explanation
Indices: 37585318--37585345 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
37585308 TACTAGTTAA
37585318 TATTATT
1 TATTATT
37585325 TATTATT
1 TATTATT
37585332 TATTATT
1 TATTATT
37585339 TATTATT
1 TATTATT
37585346 ACTACTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
TATTATT
Found at i:37585443 original size:14 final size:14
Alignment explanation
Indices: 37585424--37585452 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
37585414 GTTATCTTAT
37585424 GTAATCATATGTAA
1 GTAATCATATGTAA
37585438 GTAATCATATGTAA
1 GTAATCATATGTAA
37585452 G
1 G
37585453 GAAAGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.34
Consensus pattern (14 bp):
GTAATCATATGTAA
Found at i:37586424 original size:31 final size:29
Alignment explanation
Indices: 37586358--37586424 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 29
37586348 AATAGTTTAT
* *
37586358 ATTTTATAACTTTTAAACAGTTAAATTAA
1 ATTTTATAACTTTTAAAAAGTTAAAGTAA
37586387 ATTTTTATAA-TTTTAAAGAAGGTTAAAGTATA
1 A-TTTTATAACTTTTAAA-AA-GTTAAAGTA-A
37586419 ATTTTA
1 ATTTTA
37586425 CATTATTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 8 0.25
30 9 0.28
31 13 0.41
32 2 0.06
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (29 bp):
ATTTTATAACTTTTAAAAAGTTAAAGTAA
Found at i:37588949 original size:19 final size:18
Alignment explanation
Indices: 37588882--37588949 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 18
37588872 ATTCTTGAAA
*
37588882 AATTTTA-AAA-TTTTAA
1 AATTTTATAAATTTTTAT
** *
37588898 AATACTATATATTTTTAT
1 AATTTTATAAATTTTTAT
*
37588916 AATTTTATAATTTTTTAAT
1 AATTTTATAAATTTTT-AT
37588935 AATGTTT-TAAATTTT
1 AAT-TTTATAAATTTT
37588950 AAAATTAATT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
16 5 0.13
17 2 0.05
18 17 0.44
19 12 0.31
20 3 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (18 bp):
AATTTTATAAATTTTTAT
Found at i:37590177 original size:16 final size:17
Alignment explanation
Indices: 37590152--37590184 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
37590142 TAAATCAATA
*
37590152 AAATATTTAT-CATATT
1 AAATAATTATACATATT
37590168 AAATAATTATACATATT
1 AAATAATTATACATATT
37590185 TAATTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATAATTATACATATT
Found at i:37593449 original size:16 final size:16
Alignment explanation
Indices: 37593428--37593463 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
37593418 AATTATTATG
37593428 TATTTTTTTGAATATT-
1 TATTTTTTT-AATATTA
37593444 TATTTTTTTAATATTA
1 TATTTTTTTAATATTA
37593460 TATT
1 TATT
37593464 ATATTTTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
TATTTTTTTAATATTA
Found at i:37593451 original size:15 final size:16
Alignment explanation
Indices: 37593431--37593463 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
37593421 TATTATGTAT
37593431 TTTTTTGAATATT-TA
1 TTTTTTGAATATTATA
*
37593446 TTTTTTTAATATTATA
1 TTTTTTGAATATTATA
37593462 TT
1 TT
37593464 ATATTTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTTTGAATATTATA
Found at i:37618773 original size:24 final size:24
Alignment explanation
Indices: 37618745--37618808 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
37618735 AGAAATAATC
*
37618745 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTA
* *
37618769 TTTCAATTGAACTCTGTTTATTTA
1 TTTCAATTAAACTCTATTTATTTA
*
37618793 TTTCAATCAAACTCTA
1 TTTCAATTAAACTCTA
37618809 ATTAGTTAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.30, C:0.16, G:0.05, T:0.50
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTA
Found at i:37620329 original size:25 final size:25
Alignment explanation
Indices: 37620273--37620330 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
37620263 GCGGACACAC
*
37620273 CACAGCTCGTATAAGCTTCCTGATT
1 CACAGCTCATATAAGCTTCCTGATT
*** *
37620298 TGTAGCTTATATAAGCTTCCTGATT
1 CACAGCTCATATAAGCTTCCTGATT
37620323 CACAGCTC
1 CACAGCTC
37620331 GTGAGAGCAT
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (25 bp):
CACAGCTCATATAAGCTTCCTGATT
Found at i:37624177 original size:24 final size:23
Alignment explanation
Indices: 37624124--37624183 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
37624114 GGGATTTCAC
*
37624124 GCCTTTTTTTTTATAAGAAACTA
1 GCCTTTTTTTTTATAAGAAACGA
37624147 GCCTTTTTTTTTATAAGAAACGA
1 GCCTTTTTTTTTATAAGAAACGA
*
37624170 GCCATTTTGTTTTA
1 GCC-TTTTTTTTTA
37624184 CAAGGTGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 25 0.74
24 9 0.26
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.48
Consensus pattern (23 bp):
GCCTTTTTTTTTATAAGAAACGA
Found at i:37628086 original size:37 final size:37
Alignment explanation
Indices: 37627990--37628148 Score: 144
Period size: 37 Copynumber: 4.3 Consensus size: 37
37627980 ATCCAACTGA
* * *
37627990 AACACGCC-AATCGCTTATAAGAGCTAAACCACCTGAT
1 AACACGCCAAAT-GCTCATAAGAGCTAATCCACCCGAT
** * **
37628027 AACACATC-AATCGTTTGTAAGAGCTAATCCACCCGAT
1 AACACGCCAAAT-GCTCATAAGAGCTAATCCACCCGAT
* * * *
37628064 AACACGCCAATTGCTCCA-AAGAGCTAGTCCAACCGAA
1 AACACGCCAAATGCT-CATAAGAGCTAATCCACCCGAT
* *
37628101 AACACGCCAAATGCTCATAAGAGCTAATTCACTCGAT
1 AACACGCCAAATGCTCATAAGAGCTAATCCACCCGAT
37628138 AACACGCCAAA
1 AACACGCCAAA
37628149 ACATGAAGTA
Statistics
Matches: 98, Mismatches: 21, Indels: 6
0.78 0.17 0.05
Matches are distributed among these distances:
36 2 0.02
37 94 0.96
38 2 0.02
ACGTcount: A:0.38, C:0.30, G:0.14, T:0.18
Consensus pattern (37 bp):
AACACGCCAAATGCTCATAAGAGCTAATCCACCCGAT
Found at i:37628496 original size:7 final size:7
Alignment explanation
Indices: 37628486--37628510 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
37628476 GTCAATTCAT
37628486 AATTTTC
1 AATTTTC
37628493 AATTTTC
1 AATTTTC
37628500 AATTTTC
1 AATTTTC
37628507 AATT
1 AATT
37628511 ACACACATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTC
Found at i:37631921 original size:31 final size:31
Alignment explanation
Indices: 37631878--37631961 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
37631868 TTAGTCTTGA
37631878 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
37631908 CATATCACTGGGCCAAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
37631939 CATTTCACTGGGCTGAAGCCTTT
1 CATATCACTGGGCCGAAGCCTTT
37631962 ACTGTAAACG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 5 0.10
31 44 0.90
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:37632032 original size:42 final size:42
Alignment explanation
Indices: 37631985--37632076 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
37631975 TGGCCTATAG
* ** *
37631985 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
37632027 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
37632069 GCCCATTT
1 GCCCATTT
37632077 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:37632266 original size:26 final size:26
Alignment explanation
Indices: 37632221--37632318 Score: 171
Period size: 26 Copynumber: 3.8 Consensus size: 26
37632211 CCTCTTTAAT
37632221 AACTGGGGCA-AAGCCCTTTTCAGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
*
37632246 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCAGTA
*
37632272 AACTGGGGCATAAGCCCTTTTCGGTA
1 AACTGGGGCATAAGCCCTTTTCAGTA
37632298 AACTGGGGCATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
37632319 GCACTTCCTC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
25 10 0.14
26 59 0.86
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCAGTA
Found at i:37633205 original size:27 final size:27
Alignment explanation
Indices: 37633126--37633212 Score: 122
Period size: 27 Copynumber: 3.2 Consensus size: 27
37633116 TATTCGTCAT
* *
37633126 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCTC
*
37633153 TTTACCCTACAGGGGCTGTACGGTCTC
1 TTTACCCTACAGGGGCTTTACGGTCTC
*
37633180 TTTACCCTACAGGGGCTTTACGGTCTT
1 TTTACCCTACAGGGGCTTTACGGTCTC
37633207 TTTACC
1 TTTACC
37633213 TAATAGGGGT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 53 0.98
28 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.33
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCTC
Found at i:37633296 original size:27 final size:27
Alignment explanation
Indices: 37633243--37633557 Score: 231
Period size: 27 Copynumber: 11.6 Consensus size: 27
37633233 TTTCATCCTA
* * *
37633243 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* **
37633270 CAAGGGTATTTTAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* *** * *
37633297 CAATGGTATTTCCATAATTTTTAGAAAGT
1 CAAGGGTATTTTGGTAA-TTTTACAAA-C
* ** *
37633326 CAAGGGTATTTCT-GTAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAAC
* *
37633353 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
** * * *
37633380 TGAGGGTATTTCGATAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
37633407 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTGGTAATTTTACAAAC
* * *
37633434 TAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
** * *
37633461 TGAGGGTATTTCGGTAATTTTATAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAC
* * *
37633488 CAGGGGTATTTTAGTAATTTTACAGA-
1 CAAGGGTATTTTGGTAATTTTACAAAC
* ** *
37633514 CTAGGGTATTTTGGTAATTTTACTGAT
1 CAAGGGTATTTTGGTAATTTTACAAAC
*
37633541 CGAGGGTATTTTGGTAA
1 CAAGGGTATTTTGGTAA
37633558 ACCAAGGGCA
Statistics
Matches: 227, Mismatches: 54, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
26 25 0.11
27 175 0.77
28 14 0.06
29 13 0.06
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAC
Found at i:37633450 original size:81 final size:81
Alignment explanation
Indices: 37633354--37633551 Score: 308
Period size: 81 Copynumber: 2.5 Consensus size: 81
37633344 TTTGTAAATC
*
37633354 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAACCAGTGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAACCAGGGGTATTTT
*
37633419 GGTAATTTTACAAACT
66 AGTAATTTTACAAACT
* * *
37633435 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTTATAAACCAGGGGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAACCAGGGGTATTTT
*
37633500 AGTAATTTTACAGACT
66 AGTAATTTTACAAACT
** *
37633516 A-GGGTATTTTGGTAATTTTACTGATCGAGGGTATTT
1 AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTT
37633552 TGGTAAACCA
Statistics
Matches: 108, Mismatches: 9, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
80 32 0.30
81 76 0.70
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGATAATTTCACAAACCAGGGGTATTTT
AGTAATTTTACAAACT
Found at i:37633619 original size:54 final size:54
Alignment explanation
Indices: 37633554--37633689 Score: 164
Period size: 54 Copynumber: 2.5 Consensus size: 54
37633544 GGGTATTTTG
* * * *
37633554 GTAAACCAAGGGCATTTTAGTAATTTTATAAATCGAGGGTAAAACAGTAATTCT
1 GTAAATCAAGGGTAATTTGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCT
** * * *
37633608 GTAAATCAAGGGTAAAATGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCT
1 GTAAATCAAGGGTAATTTGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCT
* * *
37633662 ATAAATCGAGGGTACTTTGGTAATTTTA
1 GTAAATCAAGGGTAATTTGGTAATTTTA
37633690 CAATTTGAGG
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
54 66 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.32
Consensus pattern (54 bp):
GTAAATCAAGGGTAATTTGGTAATTTTATAAATCGAGGGTAAAACAGTAATTCT
Found at i:37633686 original size:27 final size:27
Alignment explanation
Indices: 37633573--37633675 Score: 152
Period size: 27 Copynumber: 3.8 Consensus size: 27
37633563 GGGCATTTTA
* *
37633573 GTAATTTTATAAATCGAGGGTAAAACA
1 GTAATTCTATAAATCGAGGGTAAAACG
* * *
37633600 GTAATTCTGTAAATCAAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAACG
*
37633627 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAACG
37633654 GTAATTCTATAAATCGAGGGTA
1 GTAATTCTATAAATCGAGGGTA
37633676 CTTTGGTAAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAACG
Found at i:37635549 original size:2 final size:2
Alignment explanation
Indices: 37635542--37635569 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
37635532 TGTTATTATG
37635542 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37635570 AAACAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37636083 original size:51 final size:51
Alignment explanation
Indices: 37636007--37636124 Score: 166
Period size: 51 Copynumber: 2.3 Consensus size: 51
37635997 CTAAGTTATT
* * *
37636007 CGGATGAAATATGAAGCTCTTGTTGAAACTAGAGCAATAAAGTAAT-ATATC
1 CGGATGAAATATGAAGCTCTTGTTGAAACCAGAACAACAAAGTAATAAT-TC
* *
37636058 CGGATGAAATATGAAGTTCTTGTTGAAGCCAGAACAACAAAGTAATAATTC
1 CGGATGAAATATGAAGCTCTTGTTGAAACCAGAACAACAAAGTAATAATTC
*
37636109 CGGATGAAGTATGAAG
1 CGGATGAAATATGAAG
37636125 AAAATTTTGG
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 58 0.97
52 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.22, T:0.25
Consensus pattern (51 bp):
CGGATGAAATATGAAGCTCTTGTTGAAACCAGAACAACAAAGTAATAATTC
Found at i:37636454 original size:15 final size:14
Alignment explanation
Indices: 37636434--37636475 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
37636424 CAATGAATTT
37636434 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
*
37636449 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
37636464 ATTGAATTATAT
1 ATTGAATTATAT
37636476 AATATATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 15 0.62
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:37636901 original size:21 final size:21
Alignment explanation
Indices: 37636877--37636938 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
37636867 GTCGTACTTG
37636877 AGGCACCTCGTGTGTCGTATC
1 AGGCACCTCGTGTGTCGTATC
* *
37636898 AGGCACCTCGTGTGTCGTTTT
1 AGGCACCTCGTGTGTCGTATC
* **
37636919 AGGCACTTTATGTGTCGTAT
1 AGGCACCTCGTGTGTCGTAT
37636939 ACTGATCAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.15, C:0.23, G:0.27, T:0.35
Consensus pattern (21 bp):
AGGCACCTCGTGTGTCGTATC
Found at i:37638221 original size:32 final size:32
Alignment explanation
Indices: 37638174--37638296 Score: 115
Period size: 32 Copynumber: 3.8 Consensus size: 32
37638164 TACCCAAGTG
* *
37638174 GTACAACTTGAAAAGGTTATGTACACTTTGTGT
1 GTAC-ACTTGAAAAGGTAAGGTACACTTTGTGT
* * *
37638207 GTACACTTGGAAAGGTTAGGTATACTTTGTGT
1 GTACACTTGAAAAGGTAAGGTACACTTTGTGT
* * *
37638239 ATAC-CATATGAAAAGGAAAGGTATACTTTGTGT
1 GTACAC-T-TGAAAAGGTAAGGTACACTTTGTGT
*
37638272 GTACCACTTGAAAAGG-AATGTACAC
1 GTA-CACTTGAAAAGGTAAGGTACAC
37638297 CTCAAGTGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
31 1 0.01
32 36 0.47
33 36 0.47
34 2 0.03
35 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.23, T:0.32
Consensus pattern (32 bp):
GTACACTTGAAAAGGTAAGGTACACTTTGTGT
Found at i:37638261 original size:33 final size:33
Alignment explanation
Indices: 37638179--37638289 Score: 118
Period size: 33 Copynumber: 3.4 Consensus size: 33
37638169 AAGTGGTACA
** * * *
37638179 ACTTGAAAAGGTTATGTACACTTTGTGTGTA-C
1 ACTTGAAAAGGAAAGGTATACTTTGTGTATACC
* **
37638211 ACTTGGAAAGGTTAGGTATACTTTGTGTATACC
1 ACTTGAAAAGGAAAGGTATACTTTGTGTATACC
*
37638244 A-TATGAAAAGGAAAGGTATACTTTGTGTGTACC
1 ACT-TGAAAAGGAAAGGTATACTTTGTGTATACC
37638277 ACTTGAAAAGGAA
1 ACTTGAAAAGGAA
37638290 TGTACACCTC
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
32 28 0.41
33 39 0.57
34 1 0.01
ACGTcount: A:0.33, C:0.11, G:0.23, T:0.32
Consensus pattern (33 bp):
ACTTGAAAAGGAAAGGTATACTTTGTGTATACC
Found at i:37646855 original size:16 final size:16
Alignment explanation
Indices: 37646836--37646909 Score: 71
Period size: 16 Copynumber: 4.7 Consensus size: 16
37646826 TAAAATAAAC
37646836 ATAAAATAAATAACAA
1 ATAAAATAAATAACAA
** *
37646852 ATAAAATAAATATTAT
1 ATAAAATAAATAACAA
* * *
37646868 AT-TATTAAAATAA-AC
1 ATAAAAT-AAATAACAA
37646883 ATAAAATAAATAACAA
1 ATAAAATAAATAACAA
37646899 ATAAAATAAAT
1 ATAAAATAAAT
37646910 GAAATAAAGA
Statistics
Matches: 45, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
15 11 0.24
16 34 0.76
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (16 bp):
ATAAAATAAATAACAA
Found at i:37646879 original size:47 final size:48
Alignment explanation
Indices: 37646813--37646909 Score: 187
Period size: 47 Copynumber: 2.0 Consensus size: 48
37646803 AATAATAATT
37646813 ATATTATTATTATTAAAATAAACATAAAATAAATAACAAATAAAATAA
1 ATATTATTATTATTAAAATAAACATAAAATAAATAACAAATAAAATAA
37646861 ATATTA-TATTATTAAAATAAACATAAAATAAATAACAAATAAAATAA
1 ATATTATTATTATTAAAATAAACATAAAATAAATAACAAATAAAATAA
37646908 AT
1 AT
37646910 GAAATAAAGA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 43 0.88
48 6 0.12
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (48 bp):
ATATTATTATTATTAAAATAAACATAAAATAAATAACAAATAAAATAA
Found at i:37648916 original size:39 final size:40
Alignment explanation
Indices: 37648871--37649002 Score: 176
Period size: 40 Copynumber: 3.3 Consensus size: 40
37648861 GCTCCTCGTT
* * *
37648871 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
37648911 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
37648950 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
37648990 CAAAGGCCTTCGG
1 CAAATGCCTTCGG
37649003 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 34 0.43
40 46 0.57
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:37649064 original size:41 final size:41
Alignment explanation
Indices: 37648987--37649064 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
37648977 TTAGTATCTC
* * *
37648987 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
37649028 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
37649065 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:37652088 original size:20 final size:18
Alignment explanation
Indices: 37652052--37652088 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
37652042 ATTGTAATTT
37652052 ATATTAATTATAAATAAG
1 ATATTAATTATAAATAAG
37652070 ATATTATATTATGAAATAA
1 ATATTA-ATTAT-AAATAA
37652089 ATCAAATGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 5 0.29
20 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (18 bp):
ATATTAATTATAAATAAG
Found at i:37652883 original size:16 final size:17
Alignment explanation
Indices: 37652862--37652894 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
37652852 TAAATGAGTT
37652862 AATTAGGAT-TAAATTG
1 AATTAGGATATAAATTG
*
37652878 AATTAGGGTATAAATTG
1 AATTAGGATATAAATTG
37652895 GATAGAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.36
Consensus pattern (17 bp):
AATTAGGATATAAATTG
Found at i:37653706 original size:44 final size:44
Alignment explanation
Indices: 37653657--37653742 Score: 129
Period size: 44 Copynumber: 2.0 Consensus size: 44
37653647 TGTTCAGGGA
*
37653657 TACTTCGACCTT-GAGTCGATGAGGCACTATAAGTGTCGTACTAT
1 TACTTCGA-CTTCGAGTCGATGAGGCACCATAAGTGTCGTACTAT
**
37653701 TACTTCGACTTCGAGTCGATGAGGCACCATGTGTGTCGTACT
1 TACTTCGACTTCGAGTCGATGAGGCACCATAAGTGTCGTACT
37653743 GCTACTGTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 3 0.08
44 35 0.92
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.31
Consensus pattern (44 bp):
TACTTCGACTTCGAGTCGATGAGGCACCATAAGTGTCGTACTAT
Found at i:37657118 original size:25 final size:25
Alignment explanation
Indices: 37657089--37657140 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
37657079 AAGAATAATT
**
37657089 TGAATATTTGATATTGCCTAATAAA
1 TGAATATTCAATATTGCCTAATAAA
* *
37657114 TGAATATTCAATATTGCTTAGTAAA
1 TGAATATTCAATATTGCCTAATAAA
37657139 TG
1 TG
37657141 TCAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (25 bp):
TGAATATTCAATATTGCCTAATAAA
Found at i:37658547 original size:3 final size:3
Alignment explanation
Indices: 37658496--37658536 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
37658486 TATGTATTAT
37658496 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
37658537 TAGTATAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:37661764 original size:37 final size:37
Alignment explanation
Indices: 37661714--37661787 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
37661704 GTCAAACATG
*
37661714 TAAGGGGGACAATTTAACATAAGTTGGCTTGTTACAA
1 TAAGGGGGACAATTTAACATAAGCTGGCTTGTTACAA
*
37661751 TAAGGGGGACAATTTAACATACGCTGGCTTGTTACAA
1 TAAGGGGGACAATTTAACATAAGCTGGCTTGTTACAA
37661788 CCTCTACCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (37 bp):
TAAGGGGGACAATTTAACATAAGCTGGCTTGTTACAA
Found at i:37663458 original size:24 final size:24
Alignment explanation
Indices: 37663428--37663588 Score: 77
Period size: 24 Copynumber: 6.6 Consensus size: 24
37663418 CTCTATAACG
37663428 GGAAGCTCATAAGAGCCATAATCA
1 GGAAGCTCATAAGAGCCATAATCA
* *
37663452 GGAAGCTCATGCA-AGCCAATAA-CG
1 GGAAGCTCAT-AAGAGCC-ATAATCA
* * *
37663476 GGTAGCTCCA-GATAGCCATATATC-
1 GGAAGCT-CATAAGAGCCATA-ATCA
* * *
37663500 GGAAGTTCA-AGCGAGCC-TTATCA
1 GGAAGCTCATA-AGAGCCATAATCA
*
37663523 GGAAGCTCACAAAGAGCCAATTAA-CA
1 GGAAGCTCA-TAAGAGCC-A-TAATCA
* *
37663549 AGAAGCTCACAAAGAGCCATAATC-
1 GGAAGCTCA-TAAGAGCCATAATCA
37663573 GGTAAGCTCATAAGAG
1 GG-AAGCTCATAAGAG
37663589 TTGTGGTGTG
Statistics
Matches: 106, Mismatches: 16, Indels: 30
0.70 0.11 0.20
Matches are distributed among these distances:
22 3 0.03
23 15 0.14
24 49 0.46
25 18 0.17
26 19 0.18
27 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (24 bp):
GGAAGCTCATAAGAGCCATAATCA
Found at i:37665691 original size:16 final size:17
Alignment explanation
Indices: 37665660--37665692 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
37665650 TTCATAAGTA
37665660 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
37665677 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
37665693 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:37666038 original size:46 final size:45
Alignment explanation
Indices: 37665988--37666129 Score: 167
Period size: 46 Copynumber: 3.1 Consensus size: 45
37665978 TGCCATAATG
* * *
37665988 TCTTTCAACTATGGTCTTACTCATTTTCTGTCAGGTTGCCATGGTA
1 TCTTTCAACAATGGTCTTATTCA-TTTCTGTCACGTTGCCATGGTA
* * * * *
37666034 TCTTTCAACCATGGTCTTGTTCATTTCATGTTACATTCCCATGGTA
1 TCTTTCAACAATGGTCTTATTCATTTC-TGTCACGTTGCCATGGTA
* * *
37666080 TCTTTCAACAATGGTCTTATTCATTCCCGTCATGTTGCCATGGTA
1 TCTTTCAACAATGGTCTTATTCATTTCTGTCACGTTGCCATGGTA
37666125 TCTTT
1 TCTTT
37666130 GTAACAGCCT
Statistics
Matches: 80, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
45 22 0.28
46 58 0.73
ACGTcount: A:0.18, C:0.23, G:0.15, T:0.44
Consensus pattern (45 bp):
TCTTTCAACAATGGTCTTATTCATTTCTGTCACGTTGCCATGGTA
Found at i:37669029 original size:28 final size:28
Alignment explanation
Indices: 37668977--37669059 Score: 121
Period size: 28 Copynumber: 2.9 Consensus size: 28
37668967 ATTTATCCGA
37668977 ATTCTGGTGTGTTTTGGATGGATTATATC
1 ATTCTGGTGTGTTTTGGA-GGATTATATC
* * *
37669006 ATTCAGGTGTGTTTGGGAGGATTATATG
1 ATTCTGGTGTGTTTTGGAGGATTATATC
*
37669034 ATACTGGTGTGTTTTGGAGGATTATA
1 ATTCTGGTGTGTTTTGGAGGATTATA
37669060 CTGGTGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 32 0.67
29 16 0.33
ACGTcount: A:0.20, C:0.05, G:0.31, T:0.43
Consensus pattern (28 bp):
ATTCTGGTGTGTTTTGGAGGATTATATC
Found at i:37669060 original size:23 final size:23
Alignment explanation
Indices: 37668980--37669073 Score: 80
Period size: 23 Copynumber: 3.6 Consensus size: 23
37668970 TATCCGAATT
37668980 CTGGTGTGTTTTGGATGGATTATA
1 CTGGTGTGTTTTGGA-GGATTATA
*
37669004 TCATTCAGGTGTGTTTGGGAGGATTATATGATA
1 -C--T--GGTGTGTTTTGGAGG---AT-T-ATA
37669037 CTGGTGTGTTTTGGAGGATTATA
1 CTGGTGTGTTTTGGAGGATTATA
37669060 CTGGTGTGTTTTGG
1 CTGGTGTGTTTTGG
37669074 TTGGACATTT
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
23 17 0.29
24 1 0.02
25 3 0.05
27 1 0.02
28 16 0.28
29 12 0.21
30 1 0.02
31 2 0.03
32 2 0.03
33 3 0.05
ACGTcount: A:0.17, C:0.05, G:0.34, T:0.44
Consensus pattern (23 bp):
CTGGTGTGTTTTGGAGGATTATA
Found at i:37670733 original size:27 final size:27
Alignment explanation
Indices: 37670685--37670843 Score: 175
Period size: 27 Copynumber: 5.9 Consensus size: 27
37670675 GCGAGGCTGC
* *
37670685 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
*
37670712 CAGATATTGTGGTAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
37670738 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
37670765 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
37670792 CAGATATATGTGGCAGAGCCACCAAAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
37670819 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
37670844 GACGCTTCCT
Statistics
Matches: 113, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
26 10 0.09
27 98 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:37670844 original size:54 final size:54
Alignment explanation
Indices: 37670703--37670846 Score: 236
Period size: 54 Copynumber: 2.7 Consensus size: 54
37670693 GTGACGAAGT
* * *
37670703 CACCAGATACAGAT-ATTGTGGTAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
37670757 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
*
37670811 CACCAAATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
37670847 GCTTCCTCCA
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 5 0.06
54 80 0.94
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:37672526 original size:121 final size:121
Alignment explanation
Indices: 37672312--37672553 Score: 466
Period size: 121 Copynumber: 2.0 Consensus size: 121
37672302 ATGGACAAAA
37672312 CTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAATTTCATATTTCATCCATTTAATTCTTTAAT
1 CTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAATTTCATATTTCATCCATTTAATTCTTTAAT
37672377 ACAAAAGACATGAAATGTCCATCATGGAACATTTACCTAAACCATTATCATGGAAC
66 ACAAAAGACATGAAATGTCCATCATGGAACATTTACCTAAACCATTATCATGGAAC
37672433 CTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAATTTCATATTTCATCCATTTAATTCTTTAAT
1 CTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAATTTCATATTTCATCCATTTAATTCTTTAAT
* *
37672498 ACAAAAGACATGAAATGTCCATCATGGAATATTTACCTAATCCATTATCATGGAAC
66 ACAAAAGACATGAAATGTCCATCATGGAACATTTACCTAAACCATTATCATGGAAC
37672554 ATTTACCTAA
Statistics
Matches: 119, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
121 119 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (121 bp):
CTTTGTTCTTTTCACCCCTTTTTCTTTTAATAAAATTTCATATTTCATCCATTTAATTCTTTAAT
ACAAAAGACATGAAATGTCCATCATGGAACATTTACCTAAACCATTATCATGGAAC
Found at i:37672548 original size:26 final size:26
Alignment explanation
Indices: 37672518--37672573 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
37672508 TGAAATGTCC
* *
37672518 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
37672544 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
37672570 ATCA
1 ATCA
37672574 ATTTGTACCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.34
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:37676389 original size:43 final size:43
Alignment explanation
Indices: 37676328--37676413 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
37676318 TGGAATGGAG
37676328 AGGAGGAGGAGGAAAATATGTATGAATATTCAGCTAACATGGC
1 AGGAGGAGGAGGAAAATATGTATGAATATTCAGCTAACATGGC
37676371 AGGAGGAGGAGGAAAATATGTATGAATATTCAGCTAACATGGC
1 AGGAGGAGGAGGAAAATATGTATGAATATTCAGCTAACATGGC
37676414 TAATTTGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (43 bp):
AGGAGGAGGAGGAAAATATGTATGAATATTCAGCTAACATGGC
Found at i:37682097 original size:36 final size:37
Alignment explanation
Indices: 37682011--37682097 Score: 99
Period size: 36 Copynumber: 2.4 Consensus size: 37
37682001 ATTTGTTAGA
*
37682011 AAAATTTTATTTTAGTGTTTTTAGTGCATTTTTTTTTG
1 AAAA-TTTATTTTAGTGTTTTTAGTGCATTATTTTTTG
**
37682049 AATTTTTATTTTAGT-TTTTTAGTGCATTAGATTTTTT-
1 AAAATTTATTTTAGTGTTTTTAGTGCATT--ATTTTTTG
37682086 AAAATTT-TTTTA
1 AAAATTTATTTTA
37682098 AATAAAAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
36 18 0.43
37 16 0.38
38 8 0.19
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (37 bp):
AAAATTTATTTTAGTGTTTTTAGTGCATTATTTTTTG
Found at i:37685127 original size:14 final size:14
Alignment explanation
Indices: 37685098--37685126 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
37685088 TAATCATCTA
37685098 TTACTATTTCAATT
1 TTACTATTTCAATT
37685112 TTACTATTT-AATT
1 TTACTATTTCAATT
37685125 TT
1 TT
37685127 TGTATATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (14 bp):
TTACTATTTCAATT
Found at i:37699918 original size:22 final size:23
Alignment explanation
Indices: 37699892--37699935 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
37699882 CCTGATCAGA
37699892 ATACGACACAT-AAGTGCCTGAC
1 ATACGACACATAAAGTGCCTGAC
37699914 ATACGACACATAAAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
37699936 TCAATAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAC
Found at i:37700199 original size:29 final size:29
Alignment explanation
Indices: 37700121--37700200 Score: 117
Period size: 28 Copynumber: 2.8 Consensus size: 29
37700111 CACCAAAATG
* * *
37700121 TCCAACCAAAACACACCAGTATCATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
*
37700150 TCC-TCCCAAACACACCAGAATAATATAA
1 TCCATCCAAAACACACCAGAATAATATAA
37700178 TCCATCCAAAACACACCAGAATA
1 TCCATCCAAAACACACCAGAATA
37700201 GCACAAAGTG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
28 24 0.53
29 21 0.47
ACGTcount: A:0.47, C:0.33, G:0.04, T:0.16
Consensus pattern (29 bp):
TCCATCCAAAACACACCAGAATAATATAA
Found at i:37702364 original size:40 final size:40
Alignment explanation
Indices: 37702320--37702402 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
37702310 TTCTATATCA
37702320 AATCATCATATACTTCCAGCACATATTCATAGAAACTTTC
1 AATCATCATATACTTCCAGCACATATTCATAGAAACTTTC
*
37702360 AATCATCATATACTTCCAGCATATATTCATAGAAACTTTC
1 AATCATCATATACTTCCAGCACATATTCATAGAAACTTTC
37702400 AAT
1 AAT
37702403 TTCTTTCATA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (40 bp):
AATCATCATATACTTCCAGCACATATTCATAGAAACTTTC
Found at i:37704882 original size:14 final size:14
Alignment explanation
Indices: 37704855--37704892 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
37704845 ACCTTTAATT
*
37704855 TTCTCTTCTCTTCTC
1 TTCT-TTCTTTTCTC
37704870 TTCTTTCTTTTCTC
1 TTCTTTCTTTTCTC
37704884 TT-TTTCTTT
1 TTCTTTCTTT
37704893 CTTCCGTCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 7 0.32
14 11 0.50
15 4 0.18
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
TTCTTTCTTTTCTC
Found at i:37704890 original size:17 final size:19
Alignment explanation
Indices: 37704854--37704895 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
37704844 AACCTTTAAT
*
37704854 TTTCTCTTCTCTTCTCTTC
1 TTTCTTTTCTCTTCTCTTC
37704873 TTTCTTTTCTCTT-T-TTC
1 TTTCTTTTCTCTTCTCTTC
37704890 TTTCTT
1 TTTCTT
37704896 CCGTCCCCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 9 0.41
18 1 0.05
19 12 0.55
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTCTTTTCTCTTCTCTTC
Found at i:37704964 original size:13 final size:14
Alignment explanation
Indices: 37704946--37704975 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
37704936 TAATTCTTTC
*
37704946 TTTTTTATTTCCTT
1 TTTTTTATTTACTT
37704960 TTTTTTATTTACTT
1 TTTTTTATTTACTT
37704974 TT
1 TT
37704976 AACAATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTATTTACTT
Found at i:37707082 original size:22 final size:22
Alignment explanation
Indices: 37707057--37707135 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
37707047 AAGTGTTATA
37707057 CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACAAATGTGCTAAT
** **
37707079 CAGAGAGCACTGACATGCTAAATAT
1 CAGAGAGCACAAATGTGCT--A-AT
37707104 CAGAGAGCACAAATGTGCTAAT
1 CAGAGAGCACAAATGTGCTAAT
*
37707126 TAGAGAGCAC
1 CAGAGAGCAC
37707136 TGACGTGCTA
Statistics
Matches: 45, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
22 26 0.58
23 1 0.02
24 1 0.02
25 17 0.38
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.18
Consensus pattern (22 bp):
CAGAGAGCACAAATGTGCTAAT
Found at i:37707108 original size:47 final size:47
Alignment explanation
Indices: 37707057--37707209 Score: 200
Period size: 47 Copynumber: 3.2 Consensus size: 47
37707047 AAGTGTTATA
*
37707057 CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACATGCTAAATAT
1 CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAAATAT
*
37707104 CAGAGAGCACAAATGTGCTAATTAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAAATAT
**** *
37707151 CAGAGAGCACTGGCGTGCTAATATTCAGAGAGCACTGGCGTGCT-AATAAT
1 CAGAGAGCACAAATGTGCT-A-A-TCAGAGAGCACTGACGTGCTAAAT-AT
37707201 CAGAGAGCA
1 CAGAGAGCA
37707210 TGCTGAAGTC
Statistics
Matches: 94, Mismatches: 8, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
47 60 0.64
48 1 0.01
49 4 0.04
50 29 0.31
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.20
Consensus pattern (47 bp):
CAGAGAGCACAAATGTGCTAATCAGAGAGCACTGACGTGCTAAATAT
Found at i:37707110 original size:25 final size:24
Alignment explanation
Indices: 37707035--37707209 Score: 164
Period size: 25 Copynumber: 7.4 Consensus size: 24
37707025 CACTAATGAA
* * *
37707035 CAGAGAGCATTGAAGTG-TTATA-
1 CAGAGAGCACTGACGTGCTAATAT
** *
37707057 CAGAGAGCACAAATGTGCT-A-AT
1 CAGAGAGCACTGACGTGCTAATAT
*
37707079 CAGAGAGCACTGACATGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
** *
37707104 CAGAGAGCACAAATGTGCTAAT-T
1 CAGAGAGCACTGACGTGCTAATAT
37707127 -AGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTGACGTGCT-AATAT
*
37707151 CAGAGAGCACTGGCGTGCTAATATT
1 CAGAGAGCACTGACGTGCTAATA-T
*
37707176 CAGAGAGCACTGGCGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAAT-AT
37707201 CAGAGAGCA
1 CAGAGAGCA
37707210 TGCTGAAGTC
Statistics
Matches: 127, Mismatches: 16, Indels: 17
0.79 0.10 0.11
Matches are distributed among these distances:
21 1 0.01
22 44 0.35
23 5 0.04
24 9 0.07
25 67 0.53
26 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.21
Consensus pattern (24 bp):
CAGAGAGCACTGACGTGCTAATAT
Found at i:37708071 original size:25 final size:25
Alignment explanation
Indices: 37708043--37708129 Score: 140
Period size: 25 Copynumber: 3.5 Consensus size: 25
37708033 GAATTCAGCA
37708043 TGCTCTCTGATTATTAGCACGCCAG
1 TGCTCTCTGATTATTAGCACGCCAG
*
37708068 TGCTCTCTGAATATTAGCACGCCAG
1 TGCTCTCTGATTATTAGCACGCCAG
*
37708093 TGCTCTCTGA-TATTTAGCACGTCAG
1 TGCTCTCTGATTA-TTAGCACGCCAG
37708118 TGCTCTCTGATT
1 TGCTCTCTGATT
37708130 GGCACATTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
24 2 0.03
25 55 0.95
26 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.20, T:0.34
Consensus pattern (25 bp):
TGCTCTCTGATTATTAGCACGCCAG
Found at i:37708160 original size:47 final size:46
Alignment explanation
Indices: 37708043--37708217 Score: 167
Period size: 47 Copynumber: 3.7 Consensus size: 46
37708033 GAATTCAGCA
* ****
37708043 TGCTCTCTGAT-TATTAGCACGCCAGTGCTCTCTGAATATTAGCACGCCAG
1 TGCTCTCT-ATAT-TTAGCACGTCAGTGCTCTCTG---ATTAGCACATTTG
*
37708093 TGCTCTCTGATATTTAGCACGTCAGTGCTCTCTGATTGGCACATTTG
1 TGCTCTCT-ATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
* * *
37708140 TGCTCTCTAATATTTAGCACGTCATTGCTATCTAATTAGCACATTTG
1 TGCTCTCT-ATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
* *
37708187 TGCTCTCTGTA--TAGCACTTCAGTGCTCTCTG
1 TGCTCTCTATATTTAGCACGTCAGTGCTCTCTG
37708218 TTCATTAGTG
Statistics
Matches: 108, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
44 16 0.15
46 2 0.02
47 58 0.54
50 31 0.29
51 1 0.01
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (46 bp):
TGCTCTCTATATTTAGCACGTCAGTGCTCTCTGATTAGCACATTTG
Found at i:37708168 original size:25 final size:25
Alignment explanation
Indices: 37708043--37708175 Score: 114
Period size: 25 Copynumber: 5.4 Consensus size: 25
37708033 GAATTCAGCA
* *
37708043 TGCTCTCTGAT-TATTAGCACGCCAG
1 TGCTCTCTAATAT-TTAGCACGTCAG
*
37708068 TGCTCTCTGAATA-TTAGCACGCCAG
1 TGCTCTCT-AATATTTAGCACGTCAG
*
37708093 TGCTCTCTGATATTTAGCACGTCAG
1 TGCTCTCTAATATTTAGCACGTCAG
* * * **
37708118 TGCTCTCT--GA-TTGGCACATTTG
1 TGCTCTCTAATATTTAGCACGTCAG
*
37708140 TGCTCTCTAATATTTAGCACGTCAT
1 TGCTCTCTAATATTTAGCACGTCAG
*
37708165 TGCTATCTAAT
1 TGCTCTCTAAT
37708176 TAGCACATTT
Statistics
Matches: 87, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
22 16 0.18
23 1 0.01
24 4 0.05
25 64 0.74
26 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (25 bp):
TGCTCTCTAATATTTAGCACGTCAG
Found at i:37723715 original size:3 final size:3
Alignment explanation
Indices: 37723709--37723733 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
37723699 ATAAGAGTAT
37723709 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
37723734 GATCTACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:37723850 original size:37 final size:37
Alignment explanation
Indices: 37723779--37723850 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 37
37723769 AAAAATATAT
* *
37723779 ATATAAAATATTTACAATAATGATGTAAATAAACAAC
1 ATATAAAATATTTACAATAATCATATAAATAAACAAC
37723816 ATATAAAATATTTGA-AATAA-CATATAAATGAAACA
1 ATATAAAATATTT-ACAATAATCATATAAAT-AAACA
37723851 TTTAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.74
38 1 0.03
ACGTcount: A:0.58, C:0.07, G:0.06, T:0.29
Consensus pattern (37 bp):
ATATAAAATATTTACAATAATCATATAAATAAACAAC
Found at i:37727847 original size:9 final size:10
Alignment explanation
Indices: 37727823--37727863 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
37727813 CAATTGTGAA
37727823 AAATAA-AAT
1 AAATAATAAT
37727832 AAAATAA-AAT
1 -AAATAATAAT
37727842 AAATAATAAT
1 AAATAATAAT
37727852 -AATAATAAT
1 AAATAATAAT
37727861 AAA
1 AAA
37727864 GAACACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATAATAAT
Found at i:37727862 original size:6 final size:5
Alignment explanation
Indices: 37727822--37727859 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
37727812 ACAATTGTGA
37727822 AAAAT AAAAT AAAAT AAAAT -AAAT AATAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AA
37727860 TAAAGAACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.13
5 16 0.52
6 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:37729844 original size:22 final size:23
Alignment explanation
Indices: 37729819--37729864 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
37729809 CAACCAAATC
37729819 AATTCA-ACATATTT-TCAAGATA
1 AATTCATACATATTTAT-AAGATA
*
37729841 AATTCATGCATATTTATAAGATA
1 AATTCATACATATTTATAAGATA
37729864 A
1 A
37729865 CGTCATCACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 14 0.67
24 1 0.05
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (23 bp):
AATTCATACATATTTATAAGATA
Found at i:37729870 original size:23 final size:23
Alignment explanation
Indices: 37729826--37729870 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
37729816 ATCAATTCAA
*
37729826 CATATTTTCAAGATAAATTCATG
1 CATATTTTCAAGATAAAGTCATG
*
37729849 CATATTTAT-AAGATAACGTCAT
1 CATATTT-TCAAGATAAAGTCAT
37729871 CACATATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.38
Consensus pattern (23 bp):
CATATTTTCAAGATAAAGTCATG
Found at i:37735213 original size:9 final size:10
Alignment explanation
Indices: 37735189--37735229 Score: 52
Period size: 9 Copynumber: 4.3 Consensus size: 10
37735179 AATTTGTGAA
37735189 AAATAA-AAT
1 AAATAATAAT
37735198 AAAATAA-AAT
1 -AAATAATAAT
37735208 AAATAATAAT
1 AAATAATAAT
37735218 -AATAATAAT
1 AAATAATAAT
37735227 AAA
1 AAA
37735230 GAACACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (10 bp):
AAATAATAAT
Found at i:37735228 original size:6 final size:5
Alignment explanation
Indices: 37735188--37735225 Score: 51
Period size: 5 Copynumber: 7.4 Consensus size: 5
37735178 CAATTTGTGA
37735188 AAAAT AAAAT AAAAT AAAAT -AAAT AATAAT AATAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AA-AAT AA
37735226 TAAAGAACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
4 4 0.13
5 16 0.52
6 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
AAAAT
Found at i:37740323 original size:16 final size:16
Alignment explanation
Indices: 37740304--37740334 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37740294 TACACCCATA
*
37740304 TATATGTACATATTTT
1 TATATATACATATTTT
37740320 TATATATACATATTT
1 TATATATACATATTT
37740335 ATCGTTTCTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATATACATATTTT
Found at i:37752123 original size:44 final size:46
Alignment explanation
Indices: 37751960--37752252 Score: 260
Period size: 46 Copynumber: 6.7 Consensus size: 46
37751950 ATAATACAGG
37751960 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
37752006 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
* * * *
37752052 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-ATAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAAT-TTCAGA
* * * * * **
37752096 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-------GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
* * * * * *
37752135 TCGTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--A-CA--TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGACCAAAGAATTTCAGA
37752176 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
* * *
37752222 TCTTATCTCCCTGAGGTTACAGCGGAGCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGA
37752253 TTGAAGCCAG
Statistics
Matches: 203, Mismatches: 28, Indels: 32
0.77 0.11 0.12
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 23 0.11
40 1 0.00
41 26 0.13
42 1 0.00
43 1 0.00
44 33 0.16
45 3 0.01
46 113 0.56
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (46 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
Found at i:37752286 original size:44 final size:44
Alignment explanation
Indices: 37752003--37752479 Score: 217
Period size: 44 Copynumber: 11.0 Consensus size: 44
37751993 AAAGAATTTC
* * * * * *
37752003 AGATCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTC
1 AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---G
* * *
37752049 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGATAG
1 AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAG
* ** * *
37752093 TA-ATC-CTATCTCCTTGAGATTACAATGGAGCGGAT--TA-A-AG
1 -AGATCTC-ATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAG
* ** * *
37752133 -GATCGT-ATCTCTCTGA-AGTTACAGTAGAGAAGATC-ACA-TCAG
1 AGATC-TCATCTCCCTGAGA-TTACAGCGGAGCAGATCGA-AGACAG
* * * * * *
37752175 -G-TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTC
1 AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---G
* * * *
37752219 AGATCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAG
1 AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAG
37752263 AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-
1 AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAG
** * * * * * *
37752306 CTATC-CTATCTCCCAGA-AGTTACAGTGGAGCGGAT-TAAAATAAG
1 AGATCTC-ATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGA-CAG
*
37752350 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-
1 AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAG
** * * * * * *
37752393 CTATC-CTATCTCCCAGA-AGTTACAGTGGAGCGGAT-TAAAATAAG
1 AGATCTC-ATCTCCCTGAGA-TTACAGCGGAGCAGATCGAAGA-CAG
*
37752437 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
1 AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
37752480 CTATCTTATC
Statistics
Matches: 325, Mismatches: 72, Indels: 70
0.70 0.15 0.15
Matches are distributed among these distances:
38 1 0.00
39 23 0.07
40 3 0.01
41 28 0.09
42 15 0.05
43 54 0.17
44 120 0.37
45 10 0.03
46 69 0.21
47 2 0.01
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (44 bp):
AGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAG
Found at i:37752417 original size:174 final size:175
Alignment explanation
Indices: 37752003--37752507 Score: 451
Period size: 174 Copynumber: 2.9 Consensus size: 175
37751993 AAAGAATTTC
* * *
37752003 AGATCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTG-AG
1 AGATCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCAGAAG
* * * ** *
37752067 ATTACAGCGGAGCAGATCAAAGA-TAGTA-ATC-CTATCTCCTTGAGATTACAATGGAGCGGAT-
64 -TTACAGCGGAGCAGATTAAA-ACAAG-AGATCTC-ATCTCCCTGAGATTACAGCGGAGCAGATC
* ** * * * * * * ** * * *
37752128 -TA-A-AGGATCGTATCTCTCTGAAGTTACAGTAGAGAAGA-TCACATCAG
125 GAAGACACTATCCTATCCCCCAGAAATTACAGTGGAGCGGATTAAAATAAG
* * * *
37752175 -G-TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGG
1 AGATCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCAGAAG
* * *
37752238 TTACAGCGGAGCAGATTGAAGCCAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
64 TTACAGCGGAGCAGATTAAAACAAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
* *
37752303 ACACTATCCTATCTCCCAGAAGTTACAGTGGAGCGGATTAAAATAAG
129 ACACTATCCTATCCCCCAGAAATTACAGTGGAGCGGATTAAAATAAG
* * * *
37752350 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A-CACTATCCTATCTCCCAGAAGT
1 AGATCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCA-GATCCTATCTCCCAGAAGT
* * * *
37752413 TACAGTGGAGCGGATTAAAATAAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
65 TACAGCGGAGCAGATTAAAACAAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
* * *
37752478 CACTATCTTATCCCCCTGAAATTGCAGTGG
130 CACTATCCTATCCCCCAGAAATTACAGTGG
37752508 CCCAAGTTGA
Statistics
Matches: 280, Mismatches: 41, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
169 1 0.00
170 106 0.38
171 3 0.01
172 1 0.00
173 3 0.01
174 125 0.45
175 6 0.02
176 2 0.01
177 33 0.12
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (175 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCAGATCCTATCTCCCAGAAGTT
ACAGCGGAGCAGATTAAAACAAGAGATCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGAC
ACTATCCTATCCCCCAGAAATTACAGTGGAGCGGATTAAAATAAG
Found at i:37752540 original size:87 final size:87
Alignment explanation
Indices: 37752176--37752507 Score: 441
Period size: 87 Copynumber: 3.8 Consensus size: 87
37752166 TCACATCAGG
* * * * * * * *
37752176 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGATCTTATCTCCCTGAGGTT
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---C-TATCCTATCTCCCAGAAGTT
* * * ***
37752240 ACAGCGGAGCAGATTGAAGCCAGAGA
62 ACAGTGGAGCGGATTAAAATAAGAGA
*
37752266 TCTCATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCAGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCAGAAGTTACAG
37752331 TGGAGCGGATTAAAATAAGAGA
66 TGGAGCGGATTAAAATAAGAGA
37752353 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCAGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCAGAAGTTACAG
37752418 TGGAGCGGATTAAAATAAGAGA
66 TGGAGCGGATTAAAATAAGAGA
* * * * *
37752440 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCTTATCCCCCTGAAATTGCAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCAGAAGTTACAG
37752505 TGG
66 TGG
37752508 CCCAAGTTGA
Statistics
Matches: 220, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
87 185 0.84
88 1 0.00
90 33 0.15
91 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (87 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCAGAAGTTACAG
TGGAGCGGATTAAAATAAGAGA
Found at i:37754082 original size:3 final size:3
Alignment explanation
Indices: 37754076--37754175 Score: 71
Period size: 3 Copynumber: 33.3 Consensus size: 3
37754066 TTTAGCCACT
* *
37754076 TTA TTA TT- TTG TTTA TT- TTA TTA TTA TTA TTA TTA TTTA CTA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * * * *
37754121 TTA TCT- TTA CTA TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
37754166 CTA TCA TTA T
1 TTA TTA TTA T
37754176 ATTTATACCT
Statistics
Matches: 76, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
2 5 0.07
3 65 0.86
4 6 0.08
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:37754108 original size:12 final size:12
Alignment explanation
Indices: 37754093--37754175 Score: 85
Period size: 12 Copynumber: 6.6 Consensus size: 12
37754083 TTTGTTTATT
*
37754093 TTATTATTATTA
1 TTATTATTACTA
37754105 TTATTATTTACTA
1 TTATTA-TTACTA
37754118 TTATTATCTTTACTA
1 TTATTA---TTACTA
* *
37754133 TTATTGTTAGTA
1 TTATTATTACTA
*
37754145 TTATTACTACTA
1 TTATTATTACTA
37754157 TTATTATTACTA
1 TTATTATTACTA
*
37754169 TCATTAT
1 TTATTAT
37754176 ATTTATACCT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
12 37 0.62
13 11 0.18
15 12 0.20
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTATTACTA
Found at i:37754351 original size:36 final size:34
Alignment explanation
Indices: 37754311--37754379 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
37754301 CATATTTTCG
*
37754311 TATATTTTATAATTTGTATATACATATACTTATATC
1 TATATTTTATAATTT-T-TATAAATATACTTATATC
* *
37754347 TATATTTTCTAATTTTTATAAATATATTTATAT
1 TATATTTTATAATTTTTATAAATATACTTATAT
37754380 GTACATACTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 15 0.50
35 1 0.03
36 14 0.47
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (34 bp):
TATATTTTATAATTTTTATAAATATACTTATATC
Found at i:37759838 original size:2 final size:2
Alignment explanation
Indices: 37759831--37759857 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
37759821 TCTAGTCTTT
37759831 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
37759858 TTGGCCTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:37760695 original size:6 final size:6
Alignment explanation
Indices: 37760681--37760714 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
37760671 ATACACACAC
*
37760681 ATACGT ATACAT ATACAT ATACAT ATACAT ATAC
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC
37760715 CAACTAAGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (6 bp):
ATACAT
Done.